Actually those are quests.
One of your main tasks is to "pacify" the sea. So you'll have to fight "rogue" pirates, three sea monsters, Sebastiano's ship and Crow fleet. Of those only Crow fleet is not timed, others are.
It's obvious for ship fights since if you read the quest logs, you know that eventually those fights will happen. It's not obvious for the first sea monster, but for the other two it is.
Just to add I had to reload twice on the third sea monster (on normal difficuly) and even then I admit I got lucky killing it. Is it perhaps too challenging, did anyone fight it on hard? IMO it was completely different difficulty from the rest of the game or I missed some strategy to kill it fast. Didn't have problems with first two.
Oh and Crow fight is a joke. QTE, me dead (sailor). Reload and restart the whole thing, for god's sakes… Pass QTE, another QTE (cannon), easy.
I HATE QTE!!! I hate no gamesaving during QTE scripted crap!!! If I wanted games like that, I'd buy Alpha Protocol.
And I'd pay twice for this game if overall combat was more challenging and the game was without bloody QTE. Will PB stop sucking up to console players already?
Thankfully Bones made another "sacrificial" comment, my hero used f word instead of me and I calmed down.